Genomics Application Notes
23.842+/-0.010. Similarly, 250 ng of total RNA was used to determine regular gene expression from either manual or Biomek automation purified RNA samples. The average Ct value for ACTB gene expression from Biomek-extracted samples was 26.06+/- 0.178 and the manually- extracted samples showed a Ct value of 26.14+/- 0.019. The average Ct value for B2M gene expression from Biomek-extracted samples was 26.42+/- 0.117 and the manually-extracted samples showed a Ct value of 26.60+/-0.062. messenger RNA extraction efficiency (Figure 3). The minus RT and controls with no template showed no amplification, indicating that the amplification resulted from miRNA and mRNA alone (data not shown). The result indicates that both extraction methods gave comparable miRNA and
Figure 2: Average RNA yields for Biomek automated and manual extraction methods.
Biomek automated extraction gave slightly higher RNA yields compared to manual extraction. To compare the RNA yields from manual extraction and Biomek automated extraction, the average RNA yield and purity was calculated from two batches of FFPE lysate prepared using the Biomek workstation and manual extraction. Figure 2 shows that the automated extraction gave an average of 7.4+/-2.16 µ g of total RNA whereas manual extraction gave an average of 4.76+/-1.46 µ g of total RNA per 10 micron individual FFPE sample. The data indicated slightly higher RNA yields for Biomek automated preparation compared to manual extraction. This is most likely due to less bead loss with extraction by the Biomek liquid handler compared to manually pipetting in multiple washing steps. Since each individual slice of FFPE samples might contain a different amount of tissue, we also observed large variation of RNA yields between samples, using either manual or Biomek extraction methods. Gene expression data demonstrates comparable miRNA and total RNArecovery from Biomek and manual extraction methods. 50 ng of total RNA was used to determine let-7c miRNA gene expression from either manual or Biomek automation purified RNA samples. The average cycle threshold (Ct) was calculated for each method. The average Ct value for let-7c gene expression from the Biomek-extracted samples was 23.722+/- 0.011 and the manually- extracted samples showed a Ct value of
Figure 3: Average Ct value for the let-7c miRNA and regular gene expression. Results of theTaqman gene expression assay for microRNA assay for let 7c (top) and ACTB and B2M (bottom) comparing the eluates generated from the manual and automation extraction methods.
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